From fc0ca72792dfc65003e10162a3619c02fd8742d1 Mon Sep 17 00:00:00 2001 From: Marcel Schilling Date: Mon, 28 Jun 2021 17:29:53 +0200 Subject: [PATCH] Fix typo: abudance -> abundance --- R/construct.R | 12 ++++++------ R/utils.R | 2 +- man/music_M.theta.Rd | 2 +- man/music_Sigma.Rd | 2 +- man/music_Sigma.ct.Rd | 2 +- man/music_Theta.Rd | 2 +- man/music_basis.Rd | 2 +- man/relative.ab.Rd | 4 ++-- 8 files changed, 14 insertions(+), 14 deletions(-) diff --git a/R/construct.R b/R/construct.R index 2ccbfde..d3ee30c 100644 --- a/R/construct.R +++ b/R/construct.R @@ -50,7 +50,7 @@ bulk_construct = function(eset, clusters, samples, select.ct = NULL){ ############ Construct Design Matrix, Library Size, and Subject-level Variation of Relative abundance for MuSiC ############ ## These functions are for cell type specific mean expression, cross-subject variance and mean library size for MuSiC deconvolution -#' Cross-subject Mean of Relative Abudance +#' Cross-subject Mean of Relative Abundance #' #' This function is for calculating the cross-subject mean of relative abundance for selected cell types. #' @@ -95,7 +95,7 @@ music_M.theta = function(x, non.zero, markers, clusters, samples, select.ct){ return(M.theta) } -#' Subject and cell type specific relative abudance +#' Subject and cell type specific relative abundance #' #' This function is for calculating the subject and cell type specific relative abundance for selected cell types. #' @@ -137,7 +137,7 @@ music_Theta <- function(x, non.zero = FALSE, clusters, samples, select.ct = NULL return(Theta = Theta) } -#' Cross-subject Corvriance of Relative Abudance +#' Cross-subject Corvriance of Relative Abundance #' #' This function is for calculating the cross-subject covariance of relative abundance for selected cell types. #' @@ -184,7 +184,7 @@ music_Sigma.ct = function(x, non.zero, markers, clusters, samples, select.ct){ return(Sigma.ct = Sigma.ct) } -#' Cross-subject Varirance of Relative Abudance +#' Cross-subject Varirance of Relative Abundance #' #' This function is for calculating the cross-subject variance of relative abundance for selected cell types. #' @@ -313,7 +313,7 @@ music_Design.matrix = function(x, non.zero, markers, clusters, samples, select.c #' * gene by cell type matrix of Design matrix #' * subject by celltype matrix of Library size #' * vector of average library size for each cell type -#' * gene by celltype matrix of average relative abudance +#' * gene by celltype matrix of average relative abundance #' * gene by celltype matrix of cross-subject variation #' #' @export @@ -336,7 +336,7 @@ music_basis = function(x, non.zero = TRUE, markers = NULL, clusters, samples, se rowSums(y)/sum(y) }), na.rm = TRUE) }) - if(verbose){message("Creating Relative Abudance Matrix...")} + if(verbose){message("Creating Relative Abundance Matrix...")} if(ct.cov){ nGenes = nrow(x); n.ct = length(unique(clusters)); diff --git a/R/utils.R b/R/utils.R index 8e0197d..08a6cda 100644 --- a/R/utils.R +++ b/R/utils.R @@ -5,7 +5,7 @@ ########################################################################## -#' Calculate relative abudance +#' Calculate relative abundance #' @param X non-negative matrix for calculate relative abundance #' @param by.col logical, default as TRUE #' @export diff --git a/man/music_M.theta.Rd b/man/music_M.theta.Rd index 16149ef..97fe535 100644 --- a/man/music_M.theta.Rd +++ b/man/music_M.theta.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/construct.R \name{music_M.theta} \alias{music_M.theta} -\title{Cross-subject Mean of Relative Abudance} +\title{Cross-subject Mean of Relative Abundance} \usage{ music_M.theta(x, non.zero, markers, clusters, samples, select.ct) } diff --git a/man/music_Sigma.Rd b/man/music_Sigma.Rd index 181cea1..6a39222 100644 --- a/man/music_Sigma.Rd +++ b/man/music_Sigma.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/construct.R \name{music_Sigma} \alias{music_Sigma} -\title{Cross-subject Varirance of Relative Abudance} +\title{Cross-subject Varirance of Relative Abundance} \usage{ music_Sigma(x, non.zero, markers, clusters, samples, select.ct) } diff --git a/man/music_Sigma.ct.Rd b/man/music_Sigma.ct.Rd index dbc9339..f8f6df2 100644 --- a/man/music_Sigma.ct.Rd +++ b/man/music_Sigma.ct.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/construct.R \name{music_Sigma.ct} \alias{music_Sigma.ct} -\title{Cross-subject Corvriance of Relative Abudance} +\title{Cross-subject Corvriance of Relative Abundance} \usage{ music_Sigma.ct(x, non.zero, markers, clusters, samples, select.ct) } diff --git a/man/music_Theta.Rd b/man/music_Theta.Rd index ebf1c23..8cdc4ce 100644 --- a/man/music_Theta.Rd +++ b/man/music_Theta.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/construct.R \name{music_Theta} \alias{music_Theta} -\title{Subject and cell type specific relative abudance} +\title{Subject and cell type specific relative abundance} \usage{ music_Theta(x, non.zero = FALSE, clusters, samples, select.ct = NULL) } diff --git a/man/music_basis.Rd b/man/music_basis.Rd index a226ec0..36565e5 100644 --- a/man/music_basis.Rd +++ b/man/music_basis.Rd @@ -40,7 +40,7 @@ a list of * gene by cell type matrix of Design matrix * subject by celltype matrix of Library size * vector of average library size for each cell type - * gene by celltype matrix of average relative abudance + * gene by celltype matrix of average relative abundance * gene by celltype matrix of cross-subject variation } \description{ diff --git a/man/relative.ab.Rd b/man/relative.ab.Rd index 7ad49de..0676f01 100644 --- a/man/relative.ab.Rd +++ b/man/relative.ab.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/utils.R \name{relative.ab} \alias{relative.ab} -\title{Calculate relative abudance} +\title{Calculate relative abundance} \usage{ relative.ab(X, by.col = TRUE) } @@ -12,5 +12,5 @@ relative.ab(X, by.col = TRUE) \item{by.col}{logical, default as TRUE} } \description{ -Calculate relative abudance +Calculate relative abundance }